ArticleDatabase : the journal of biological databases and curation2011
The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data.
Article in Database : the journal of biological databases and curation, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Genome Database for Vaccinium: a knowledgebase for genetics, genomics, and breeding research.Genetics · 2026Article
- Post-composing ontology terms for efficient phenotyping in plant breeding.Database : the journal of biological databases and curation · 2025Article
- Building resource-efficient community databases using open-source software.Database : the journal of biological databases and curation · 2025Article
- Collecting and managing in situ banana genetic resources information (Musa spp.) using online resources and citizen science.Database : the journal of biological databases and curation · 2024Article
- Methodology for Constructing a Knowledgebase for Plant Gene Regulation Information.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Breedbase: a digital ecosystem for modern plant breeding.G3 (Bethesda, Md.) · 2022Article
- A PostgreSQL Tripal solution for large-scale genotypic and phenotypic data.Database : the journal of biological databases and curation · 2021Article
- Transforming the study of organisms: Phenomic data models and knowledge bases.PLoS computational biology · 2020Review
- Article
- Cyberinfrastructure and resources to enable an integrative approach to studying forest trees.Evolutionary applications · 2020Article
- Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases.Database : the journal of biological databases and curation · 2019Article
- Modeling Crop Genetic Resources Phenotyping Information Systems.Frontiers in plant science · 2019Article
- Tripal MapViewer: A tool for interactive visualization and comparison of genetic maps.Database : the journal of biological databases and curation · 2019Article
- SeedUSoon: A New Software Program to Improve Seed Stock Management and Plant Line Exchanges between Research Laboratories.Frontiers in plant science · 2017Article
- Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases.Database : the journal of biological databases and curation · 2017Article
- Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data.Database : the journal of biological databases and curation · 2016Article
- Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado.Database : the journal of biological databases and curation · 2016Article
- The Sol Genomics Network (SGN)--from genotype to phenotype to breeding.Nucleic acids research · 2015Article
- solGS: a web-based tool for genomic selection.BMC bioinformatics · 2014Article
- The Genome Database for Rosaceae (GDR): year 10 update.Nucleic acids research · 2014Article
Corrections and comments
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Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Linking phenotypic with genotypic diversity has become a major requirement for basic and applied genome-centric biological research. To meet this need, a comprehensive database backend for efficiently storing, querying and analyzing large experimental data sets is necessary. Chado, a generic, modular, community-based database schema is widely used in the biological community to store information associated with genome sequence data. To meet the need to also accommodate large-scale phenotyping and genotyping projects, a new Chado module called Natural Diversity has been developed. The module strictly adheres to the Chado remit of being generic and ontology driven. The flexibility of the new module is demonstrated in its capacity to store any type of experiment that either uses or generates specimens or stock organisms. Experiments may be grouped or structured hierarchically, whereas any kind of biological entity can be stored as the observed unit, from a specimen to be used in genotyping or phenotyping experiments, to a group of species collected in the field that will undergo further lab analysis. We describe details of the Natural Diversity module, including the design approach, the relational schema and use cases implemented in several databases.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.